fix: add missing infer script and post-publication fixes

aphp / eds-pseudo

EDS-Pseudo is a hybrid model for detecting personally identifying entities in clinical reports

https://aphp.github.io/eds-pseudo

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fix: add missing infer script and post-publication fixes #6

Closed percevalw closed 1 year ago

percevalw commented 1 year ago

Description

Some fixes to enable training the model:

committed the missing script infer.py
changed config default bert model to camembert-base
put config.cfg as a dependency, not params
default to cpu training
allow for missing metadata (i.e. omop's note_class_source_value)

Checklist

[] If this PR is a bug fix, the bug is documented in the test suite.
[] Changes were documented in the changelog (pending section).
[] If necessary, changes were made to the documentation.

codecov-commenter commented 1 year ago

Codecov Report

Patch and project coverage have no change.

Comparison is base (d7f177f) 97.70% compared to head (6196690) 97.70%.

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #6 +/- ## ======================================= Coverage 97.70% 97.70% ======================================= Files 11 11 Lines 348 348 ======================================= Hits 340 340 Misses 8 8 ```

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